Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds

2014 ◽  
Author(s):  
Kary Ocana ◽  
Silvia Benza ◽  
Daniel De Oliveira ◽  
Jonas Dias ◽  
Marta Mattoso
Keyword(s):  
Molecular Docking ◽  
Large Scale ◽  
Receptor Ligand

scholarly journals Exploiting the Reverse Vaccinology Approach to Design Novel Subunit Vaccine against Ebola Virus

2020 ◽  
Author(s):  
Md. Asad Ullah ◽  
Bishajit Sarkar ◽  
Syed Sajidul Islam
Keyword(s):  
Molecular Docking ◽  
Mhc Class Ii ◽  
Large Scale ◽  
Matrix Protein ◽  
Ebola Virus ◽  
Rna Virus ◽  
Docking Study ◽  
Dynamics Simulation ◽  
Molecular Docking Study ◽  
Class I Mhc

AbstractEbola virus is a highly pathogenic RNA virus that causes haemorrhagic fever in human. With very high mortality rate, Ebola virus is considered as one of the dangerous viruses in the world. Although, the Ebola outbreaks claimed many lives in the past, no satisfactory treatment or vaccine have been discovered yet to fight against Ebola. For this reason, in this study, various tools of bioinformatics and immunoinformatics were used to design possible vaccines against Zaire Ebola virus strain Mayinga-76. To construct the vaccine, three potential antigenic proteins of the virus, matrix protein VP40, envelope glycoprotein and nucleoprotein were selected against which the vaccines would be designed. The MHC class-I, MHC class-II and B-cell epitopes were determined and after robust analysis through various tools and molecular docking analysis, three vaccine candidates, designated as EV-1, EV-2 and EV-3, were constructed. Since the highly conserved epitopes were used for vaccine construction, these vaccine constructs are also expected to be effective on other strains of Ebola virus like strain Gabon-94 and Kikwit-95. Next, the molecular docking study on these vaccine constructs were analyzed by molecular docking study and EV-1 emerged as the best vaccine construct. Later, molecular dynamics simulation study revealed the good performances as well as good stability of the vaccine protein. Finally, codon adaptation and in silico cloning were conducted to design a possible plasmid (pET-19b plasmid vector was used) for large scale, industrial production of the EV-1 vaccine.

Large-scale transcriptional profiling of chemosensory neurons identifies receptor-ligand pairs in vivo

2015 ◽  
Vol 18 (10) ◽  
pp. 1455-1463 ◽  
Author(s):  
Benoît von der Weid ◽  
Daniel Rossier ◽  
Matti Lindup ◽  
Joël Tuberosa ◽  
Alexandre Widmer ◽  
...  
Keyword(s):  
Large Scale ◽  
Transcriptional Profiling ◽  
Receptor Ligand ◽  
Chemosensory Neurons

scholarly journals Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.

2001 ◽  
Vol 48 (1) ◽  
pp. 131-135 ◽  
Author(s):  
R Slusarz ◽  
R Kaźmierkiewicz ◽  
A Giełdoń ◽  
B Lammek ◽  
J Ciarkowski
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Ligand Binding ◽  
Effective Procedure ◽  
Amino Acid Residues ◽  
Receptor Ligand ◽  
Docking Simulations ◽  
Oxytocin Receptors ◽  
Developing Area

Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.

Diverse polyketides and alkaloids from Penicillium sp. KHMM: structural elucidation, biological and molecular docking studies

2019 ◽  
Vol 74 (5-6) ◽  
pp. 131-137 ◽  
Author(s):  
Abdelaaty Hamed ◽  
Mohamed Ismail ◽  
Mohammad M. El-Metwally ◽  
Marcel Frese ◽  
Tarek M.A. Ibrahim ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Large Scale ◽  
Carcinoma Cell ◽  
Docking Studies ◽  
In Vitro Cytotoxicity ◽  
Cervix Carcinoma ◽  
Pathogenic Microorganisms ◽  
Mass Measurements ◽  
Human Cervix

Abstract As a continuation of our earlier research concerning the investigation of microbial bioactive secondary metabolites from the terrestrial Penicillium sp.KH Link 1809 isolate KHMM, the fungus was re-cultivated on a large scale to explore its bioactive compounds intensively. Fifteen compounds, including seven alkaloids (1–7), one sesquiterpene (8), an acetylenic system (9), two sterols, and sphengolipid, were identified. Their structures were established on the bases of extensive one- and two-dimensional nuclear magnetic resonance and mass measurements, and by comparison with literature data. The antimicrobial activity of the fungal extract and the corresponding compounds were studied using a panel of pathogenic microorganisms, and their in vitro cytotoxicity against the human cervix carcinoma cell line (KB-3-1) was reported as well. The molecular docking of the isolated compounds showed promising affinities for the alkaloidal compounds 4–6 towards α, β tubulins.

scholarly journals Integrative Analysis to Uncover the Molecular Mechanisms of Caesalpinia sappan L. for Anti-Cancer Activity

2021 ◽  
Vol 16 (11) ◽  
pp. 1934578X2110399
Author(s):  
Bing Liu ◽  
Hao Lian
Keyword(s):  
Molecular Docking ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Network Pharmacology ◽  
Dependent Manner ◽  
Genomic Databases ◽  
Caesalpinia Sappan ◽  
Dose Dependent

Objectives: Caesalpinia Sappan L. is a traditional Chinese medicine with a long history. Recent studies have confirmed that Sappan has an antitumor effect, but its specific mechanism is still unclear. Methods: In this study, we used network pharmacology to predict the target and signal pathway of Sappan. In addition, the Cancer Genome Atlas and cancer cell lines encyclopedia large-scale genomic databases were used to analyze the relationship between different subtypes of Akt. Based on molecular docking technology, the interaction mode between small molecule compounds and protein targets was explored. Finally, we studied the effect of Sappan on Akt protein expression by Western blot in vitro. Results: AKT1 and AKT2 were significantly expressed in breast cancer cells, but they were significantly different from AKT3. Finally, molecular docking analysis showed that (3R,5R)-1,3,4,5-tetrakis(((E)-3-(3,4-dihydroxyphenyl)acryloyl)oxy)cyclohexane-1-carboxylic acid had a very ideal binding mode with Akt. Subsequent experiments showed that Sappan extract could induce apoptosis of HepG2 cells in a dose-dependent manner, and down regulate the phosphorylation level of Akt protein thr308 in a dose-dependent manner. Conclusions: This study provides new ideas for Sappan's anticancer research through the strategy of system pharmacology.

scholarly journals In silico approach of receptor-ligand binding and interaction: Established phytoligands from Tagetes errecta Linn. against bacterial β-glucosidase receptor

2019 ◽  
Vol 9 (1-s) ◽  
pp. 125-131
Author(s):  
Madhumita Lahiri ◽  
Partha Talukdar ◽  
Soumendra Nath Talapatra
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ligand Binding ◽  
Antimicrobial Agents ◽  
Volatile Oil ◽  
Competitive Inhibitor ◽  
Ornamental Plant ◽  
Binding Interaction ◽  
Receptor Ligand ◽  
Energy Value

The medicinal plant, Tagetes errecta Linn. is a common ornamental plant and leaves of this plant are containing phytochemicals (volatile oil) that inhibit the growth of bacteria, fungi and known natural antimicrobial agents. The objective of the present study was to detect receptor-ligand binding energy and interaction through molecular docking for phytoligands established in the leaves of T. errecta against β-glucosidase receptor (PDB ID: 3AHZ). Molecular docking was performed by using PyRx (Version 0.8) for the structure-based virtual screening and visualized the interaction in the molecular graphic laboratory (MGL) tool (Version 1.5.6). Among 25 phytochemicals and 2 synthetic compounds (Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol), binding energy value was obtained highest in Bicyclogermacrene (-6.4 Kcal/mol) and lowest in Octanol (-4.4 Kcal/mol) and Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol showed -6.7 Kcal/mol and -3.5 Kcal/mol all of these showed no hydrogen bonding. The binding interaction of target protein with this phytocompound found binding at the mouth of the active site may be treated as competitive inhibitor. In conclusion, phytocompound Bicyclogermacrene can be alternative of synthetic fungicide as per binding energy value and interaction. It is suggesting further pharmacological and toxicological assay with this phytocompound after isolation from ornamental plant (T. errecta).

scholarly journals Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking

Foods ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 67
Author(s):  
Samo Lešnik ◽  
Urban Bren
Keyword(s):  
Molecular Docking ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Biological Activities ◽  
Data Bank ◽  
Docking Study ◽  
Antimicrobial Activities ◽  
Carnosic Acid ◽  
Molecular Docking Study

Rosemary (Rosmarinus officinalis L.) represents a medicinal plant known for its various health-promoting properties. Its extracts and essential oils exhibit antioxidative, anti-inflammatory, anticarcinogenic, and antimicrobial activities. The main compounds responsible for these effects are the diterpenes carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid. However, surprisingly little is known about the molecular mechanisms responsible for the pharmacological activities of rosemary and its compounds. To discern these mechanisms, we performed a large-scale inverse molecular docking study to identify their potential protein targets. Listed compounds were separately docked into predicted binding sites of all non-redundant holo proteins from the Protein Data Bank and those with the top scores were further examined. We focused on proteins directly related to human health, including human and mammalian proteins as well as proteins from pathogenic bacteria, viruses, and parasites. The observed interactions of rosemary compounds indeed confirm the beforementioned activities, whereas we also identified their potential for anticoagulant and antiparasitic actions. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using both redocking procedures and retrospective metrics.

scholarly journals Redesigning Vina@QNLM for Ultra-Large-Scale Molecular Docking and Screening on a Sunway Supercomputer

2021 ◽  
Vol 9 ◽  
Author(s):  
Hao Lu ◽  
Zhiqiang Wei ◽  
Cunji Wang ◽  
Jingjing Guo ◽  
Yuandong Zhou ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Large Scale ◽  
Management Process ◽  
Processor Architecture ◽  
Multicore Processor ◽  
Heterogeneous Multicore ◽  
Lead Compounds ◽  
Parallel Processes ◽  
Process Elements ◽  
Process Element

Ultra-large-scale molecular docking can improve the accuracy of lead compounds in drug discovery. In this study, we developed a molecular docking piece of software, Vina@QNLM, which can use more than 4,80,000 parallel processes to search for potential lead compounds from hundreds of millions of compounds. We proposed a task scheduling mechanism for large-scale parallelism based on Vinardo and Sunway supercomputer architecture. Then, we readopted the core docking algorithm to incorporate the full advantage of the heterogeneous multicore processor architecture in intensive computing. We successfully expanded it to 10, 465, 065 cores (1,61,001 management process elements and 0, 465, 065 computing process elements), with a strong scalability of 55.92%. To the best of our knowledge, this is the first time that 10 million cores are used for molecular docking on Sunway. The introduction of the heterogeneous multicore processor architecture achieved the best speedup, which is 11x more than that of the management process element of Sunway. The performance of Vina@QNLM was comprehensively evaluated using the CASF-2013 and CASF-2016 protein–ligand benchmarks, and the screening power was the highest out of the 27 pieces of software tested in the CASF-2013 benchmark. In some existing applications, we used Vina@QNLM to dock more than 10 million molecules to nine rigid proteins related to SARS-CoV-2 within 8.5 h on 10 million cores. We also developed a platform for the general public to use the software.

scholarly journals Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Maciej Pawel Ciemny ◽  
Aleksander Debinski ◽  
Marta Paczkowska ◽  
Andrzej Kolinski ◽  
Mateusz Kurcinski ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Conformational Changes ◽  
Large Scale
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